You have two folder for WINDOWS?
Type this in Run dialog (StartMenu-Run) : "cmd". It will open a command prompt. In the command prompt type "%WINDIR%", the folder you will see is your Windows folder. You can safely delete the a other one. Make sure you have not stored anything in the other folder.
Most probably, you have installed Windows when there was a folder "C:\Windows" already on your harddisk, so setup created "C:\Windows.0" for new Windows installation.
Before trying to delete the non-Windows folder (most probably C:\Windows), just rename it and see what happens. If it is required by some programs? Alsi check its contents, if you need them.
Hope this helps you